Atypical Porcine Pestiviruses: Relationships and Conserved Structural Features

Figures

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  Figure 1. (A) Pestivirus genome organisation, polyprotein processing and special traits of viruses isolated from harbour porpoises (B) as well as swine and bats (C). The structural proteins are coloured in shades of blue. NS = non-structural protein.

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  Figure 2. Neighbour joining tree (1000 replicates) of the polyprotein of representatives of different pestivirus species and isolates. GenBank accession numbers of the isolates are: APPV AQM73625, Aydin-like pestivirus YP_006860588.1, bat pestivirus AYV99177.1, BDV AAC16444.1, Bungowannah virus YP_008992092.1, BVDV-1 AYA62524.1, BVDV-2 AMO65207.1, BVDV-3 AGO04420.1, CSFV CAA65386.1, LINDA virus YP_009407716.1, Norway rat pestivirus YP_009109567.1, pestivirus giraffe NP_620053.1, pestivirus isolate reindeer AAF02524.2, phocoena pestivirus QFQ60724.1, pronghorn antelope pestivirus YP_009026415.1, rodent pestivirus ATP66856.1 and ATP66855.1. The phylogenetic tree was generated with CLC Sequence Viewer and the multiple sequence alignment with ClustalW.

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  Figure 3. Neighbour Joining tree of full ORF coding sequences of APPV isolates available from GenBank. The tree was generated from 1000 replicates and a bat pestivirus isolate from China has been used as an outgroup (MH282908). GenBank accession numbers as well as the year of isolation are given for each isolate in the tree. Isolates are coloured according to geographic origin. Flags indicate the closest related full ORF sequence in case no full ORF coding sequences are available from a country where APPV has been reported. The phylogenetic tree was generated with CLC Sequence Viewer and the multiple sequence alignment with ClustalW.

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  Figure 4. Crystal structure of CSFV Npro. (A) Cartoon representation of Npro (PDB code 4H9J). On the left, Npro is coloured from the N terminus (blue) to the C terminus (red). On the right, Npro is coloured according to sequence conservation from white (non-conserved) to red (conserved). (B) Location of important residues in Npro, H69 and C89 (left, APPV numbering) and the TRASH motif (right) are drawn as sticks. Figure 4, Figure 5, Figure 6, Figure 7 and Figure 8 were prepared with PyMOL (The PyMOL Molecular Graphics System, Schrödinger, LLC., New York, NY, USA).

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  Figure 5. Crystal structure of Erns. (A) Cartoon representation of Erns (PDB code 4DWC). On the left, Erns is coloured from the N terminus (blue) to the C terminus (red). On the right, Erns is coloured according to sequence conservation from white (non-conserved) to red (conserved). (B) Disulfide bridges and residues of the active site are shown as sticks.

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  Figure 6. Crystal structure of BVDV E2. (A) Cartoon representation of E2 (PDB code 2YQ2). On the left, E2 is coloured from the N terminus (blue) to the C terminus (red). On the right, E2 is coloured according to sequence conservation from white (non-conserved) to red (conserved). (B) Residues H70 and N186 from the DA and DD domains respectively, are shown as sticks.

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  Figure 7. Crystal structure of CSFV NS3. (A) Cartoon representation of NS3 (PDB code 5WX1). On the left, NS3 is coloured from the N terminus (blue) to the C terminus (red). On the right, NS3 is coloured according to sequence conservation from white (non-conserved) to red (conserved). (B) On the left, residues forming the catalytic triad are shown as sticks; on the right, the Walker motifs A and B are coloured in blue and magenta respectively.

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  Figure 8. Crystal structure of NS5B. (A) Cartoon representation of NS5B (PDB code 5Y6R). On the left, NS3 is coloured from the N terminus (blue) to the C terminus (red). On the right, NS5B is coloured according to sequence conservation from white (non-conserved) to red (conserved). (B) The catalytic aspartate residues (D345 and S350) as well as the GDD motif (447–449) are shown as sticks. Important finger domain residues (K282, K283, R285 and I287) are labelled in italics.